[2023-03-15 23:38:54,916] [INFO] DFAST_QC pipeline started.
[2023-03-15 23:38:54,919] [INFO] DFAST_QC version: 0.5.7
[2023-03-15 23:38:54,919] [INFO] DQC Reference Directory: /var/lib/cwl/stg19b82b04-2dfd-4e08-85e0-427ead934965/dqc_reference
[2023-03-15 23:38:56,041] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-15 23:38:56,041] [INFO] Task started: Prodigal
[2023-03-15 23:38:56,042] [INFO] Running command: cat /var/lib/cwl/stgdb41381b-4c9d-4109-a663-9af842dd3115/OceanDNA-b24253.fa | prodigal -d OceanDNA-b24253/cds.fna -a OceanDNA-b24253/protein.faa -g 11 -q > /dev/null
[2023-03-15 23:39:06,363] [INFO] Task succeeded: Prodigal
[2023-03-15 23:39:06,364] [INFO] Task started: HMMsearch
[2023-03-15 23:39:06,364] [INFO] Running command: hmmsearch --tblout OceanDNA-b24253/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg19b82b04-2dfd-4e08-85e0-427ead934965/dqc_reference/reference_markers.hmm OceanDNA-b24253/protein.faa > /dev/null
[2023-03-15 23:39:06,541] [INFO] Task succeeded: HMMsearch
[2023-03-15 23:39:06,541] [WARNING] Found 5/6 markers. [/var/lib/cwl/stgdb41381b-4c9d-4109-a663-9af842dd3115/OceanDNA-b24253.fa]
[2023-03-15 23:39:06,596] [INFO] Query marker FASTA was written to OceanDNA-b24253/markers.fasta
[2023-03-15 23:39:06,597] [INFO] Task started: Blastn
[2023-03-15 23:39:06,597] [INFO] Running command: blastn -query OceanDNA-b24253/markers.fasta -db /var/lib/cwl/stg19b82b04-2dfd-4e08-85e0-427ead934965/dqc_reference/reference_markers.fasta -out OceanDNA-b24253/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-15 23:39:07,136] [INFO] Task succeeded: Blastn
[2023-03-15 23:39:07,143] [INFO] Selected 26 target genomes.
[2023-03-15 23:39:07,143] [INFO] Target genome list was writen to OceanDNA-b24253/target_genomes.txt
[2023-03-15 23:39:07,158] [INFO] Task started: fastANI
[2023-03-15 23:39:07,158] [INFO] Running command: fastANI --query /var/lib/cwl/stgdb41381b-4c9d-4109-a663-9af842dd3115/OceanDNA-b24253.fa --refList OceanDNA-b24253/target_genomes.txt --output OceanDNA-b24253/fastani_result.tsv --threads 1
[2023-03-15 23:39:23,086] [INFO] Task succeeded: fastANI
[2023-03-15 23:39:23,087] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg19b82b04-2dfd-4e08-85e0-427ead934965/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-15 23:39:23,087] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg19b82b04-2dfd-4e08-85e0-427ead934965/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-15 23:39:23,087] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-03-15 23:39:23,087] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-03-15 23:39:23,087] [INFO] DFAST Taxonomy check final result
--------------------------------------------------------------------------------
organism_name	strain	accession	taxid	species_taxid	relation_to_type	validated	ani	matched_fragments	total_fragments	ani_threshold	status
--------------------------------------------------------------------------------
[2023-03-15 23:39:23,094] [INFO] DFAST Taxonomy check result was written to OceanDNA-b24253/tc_result.tsv
[2023-03-15 23:39:23,107] [INFO] ===== Taxonomy check completed =====
[2023-03-15 23:39:23,107] [INFO] ===== Start completeness check using CheckM =====
[2023-03-15 23:39:23,107] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg19b82b04-2dfd-4e08-85e0-427ead934965/dqc_reference/checkm_data
[2023-03-15 23:39:23,110] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-15 23:39:23,122] [INFO] Task started: CheckM
[2023-03-15 23:39:23,122] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b24253/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b24253/checkm_input OceanDNA-b24253/checkm_result
[2023-03-15 23:39:53,472] [INFO] Task succeeded: CheckM
[2023-03-15 23:39:53,472] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 78.03%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-15 23:39:53,698] [INFO] ===== Completeness check finished =====
[2023-03-15 23:39:53,698] [INFO] ===== Start GTDB Search =====
[2023-03-15 23:39:53,698] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b24253/markers.fasta)
[2023-03-15 23:39:53,699] [INFO] Task started: Blastn
[2023-03-15 23:39:53,699] [INFO] Running command: blastn -query OceanDNA-b24253/markers.fasta -db /var/lib/cwl/stg19b82b04-2dfd-4e08-85e0-427ead934965/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b24253/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-15 23:39:54,437] [INFO] Task succeeded: Blastn
[2023-03-15 23:39:54,448] [INFO] Selected 24 target genomes.
[2023-03-15 23:39:54,448] [INFO] Target genome list was writen to OceanDNA-b24253/target_genomes_gtdb.txt
[2023-03-15 23:39:54,476] [INFO] Task started: fastANI
[2023-03-15 23:39:54,476] [INFO] Running command: fastANI --query /var/lib/cwl/stgdb41381b-4c9d-4109-a663-9af842dd3115/OceanDNA-b24253.fa --refList OceanDNA-b24253/target_genomes_gtdb.txt --output OceanDNA-b24253/fastani_result_gtdb.tsv --threads 1
[2023-03-15 23:40:08,448] [INFO] Task succeeded: fastANI
[2023-03-15 23:40:08,452] [INFO] Found 5 fastANI hits (0 hits with ANI > circumscription radius)
[2023-03-15 23:40:08,453] [INFO] GTDB search result
--------------------------------------------------------------------------------
accession	gtdb_species	ani	matched_fragments	total_fragments	gtdb_taxonomy	ani_circumscription_radius	mean_intra_species_ani	min_intra_species_ani	mean_intra_species_af	min_intra_species_af	num_clustered_genomes	status
GCA_002731375.1	s__GCA-2731375 sp002731375	77.1924	71	462	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__GCA-2731375;f__GCA-2731375;g__GCA-2731375	95.0	99.58	99.58	0.91	0.91	2	-
GCA_018660265.1	s__GCA-2731375 sp018660265	76.4976	69	462	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__GCA-2731375;f__GCA-2731375;g__GCA-2731375	95.0	99.92	99.87	0.96	0.94	11	-
GCA_018667855.1	s__GCA-2731375 sp018667855	76.4799	101	462	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__GCA-2731375;f__GCA-2731375;g__GCA-2731375	95.0	99.62	99.58	0.85	0.84	3	-
GCA_018701215.1	s__GCA-2731375 sp018701215	76.2372	81	462	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__GCA-2731375;f__GCA-2731375;g__GCA-2731375	95.0	99.97	99.95	0.98	0.97	15	-
GCA_016776605.1	s__GCA-2731375 sp016776605	76.0995	65	462	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__GCA-2731375;f__GCA-2731375;g__GCA-2731375	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-03-15 23:40:08,458] [INFO] GTDB search result was written to OceanDNA-b24253/result_gtdb.tsv
[2023-03-15 23:40:08,464] [INFO] ===== GTDB Search completed =====
[2023-03-15 23:40:08,471] [INFO] DFAST_QC result json was written to OceanDNA-b24253/dqc_result.json
[2023-03-15 23:40:08,471] [INFO] DFAST_QC completed!
[2023-03-15 23:40:08,471] [INFO] Total running time: 0h1m14s